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After the seeming defeat of the dark archonUlrezaj on the protoss homeworld of Aiur, Jake and Rosemary become separated as they flee through the newly repaired warp gate. Rosemary finds herself with the other refugee protoss on Shakuras, while Jake is catapulted elsewhere. But Jake does not have long to live: their enemies are regrouping, and Zamara’s essence must be separated from Jake’s mind before time runs out.

Jake knows he must survive long enough for Zamara to pass on her vital secret. But which faction—Valerian, zerg, or the recovered and increasingly powerful Ulrezaj—will find them first? His only hope rests with the powerful and legendary Zeratul, but as Jake is about to learn…even a dark templar can have a crisis of faith.

The Alys'aril, "Sanctuary of Wisdom", was located on the moon of Ehlna, the first place settled by the Dark Templar after their strife due to the presence of a xel'nagawarp gate. The energies there modified khaydarin crystals to be efficient at holding memories, which the Dark Templar used as a technological alternative to the preservers they did not have. The "Well of Knowledge" held knowledge forbidden to all but the highest-ranking alysaar ("Seekers of Wisdom"). A promising, young alysaar, Ulrezaj, took to accessing that information without permission.

Jake Ramsey, and thus Zamara, were the last ones to flee through the warp gate. Rosemary Dahl and a number of former [[Tal'darim] (Aiur)|Tal'darim]] arrived on Shakuras. The gate guards, shocked that they had arrived from Aiur, redirected Ramsey and shut down the gate from all travel. They refused to believe Dahl or the Tal'darim, as they did not trust terrans and their minds had been altered by Sundrop.

Ramsey and Zamara were redirected to an icy planet for a short time; Zamara believed that Zeratul would be capable of helping them, and so they journeyed to Zeratul's private sanctuary, a calming planet with pink skies. There, they met Zeratul and discover that he has lived there in exile for crimes of which he wouldn't speak. After several days of trying to converse with him, they succeeded by exploiting his curiosity with the tale of Zamara's attack and how she transferred her mind and memories into Ramsey on Nemaka. Zeratul then told the tale of how he killed his matriarch, Raszagal. Ramsey pressed him that he is actually disappointing Raszagal by not leading her people, angering Zeratul who sent them away.

In time, Zeratul realizes that Ramsey was right. He told them of his first encounter with Ulrezaj, and then requested that Zamara share the piece of knowledge she has been safeguarding so carefully. She revealed that though extremely long-lived, the xel'naga are not immortal and do not breed. At the end of their life cycles, they find two races and direct their evolution; one to have purity of form, the other purity of essence. Once each change was made, they would be combined naturally and peacefully, becoming the xel'naga "reborn". This was "as natural to them as breathing is to [terrans], or as gathering nutrients is to [protoss]". Zeratul shared the tale of the hybrids that were created by Samir Duran. They traveled to the moon Ehlna and the settlement of Alys'aril, the place where the dark templar store their memories in special khaydarin crystals.

Rosemary Dahl was held prisoner on Shakuras by ExecutorSelendis until the Tal'darim could be purged of Sundrop and their claims verified. She befriended former Tal'darim and craftsman Vartanil who, in the absence of Zamara, swore to follow Dahl.

Selendis confirmed the story and, pointing out that the only female terran the protoss had experience with was Kerrigan, brought her to an audience with the Hierarchy, the rulers of the protoss, where they convinced Artanis and some of the other rulers that rescuing Jake Ramsey and Zamara was worth the risk. Mohandar, leader of the Nerazim, told them of the Alys'aril at Ehlna, where Ramsey would need to travel to separate Zamara from his mind. The site was sacred to the Nerazim, so he insisted only a small group travel there.

Ulrezaj had been weakened by the psionic storm attack and tried to take shelter in the caverns beneath Aiur, but he was shadowed by the forces of Valerian Mengsk and hounded by the zerg. Given little time to refresh himself, he took command of a xel'naga vessel hidden in the caverns and fled to Ehlna. His enemies followed him, hoping to claim Zamara before Ulrezaj could.

At the Alys'aril, Krythkal and his top students began to transfer Zamara into the powerful khaydarin crystal from Aiur through a sacred ritual. It was nearly interrupted by Ethan Stewart. Selendis convinced him to wait until the ritual was completed, but Stewart insisted on sending a single hydralisk to watch over the proceedings. Meanwhile Rosemary Dahl and Vartanil repaired an ancient ship so they could take away the crystals filled with memories.

Ulrezaj, having replenished himself underwater, attacked, devastating the zerg force. A Dominion task force carrying Valerian Mengsk, but under the orders of Arcturus, also appeared and began fighting.

Within the memory transfer, Zamara expected to die, and only her memories would be preserved. However, the crystal they were using had not been modified by Ehlna's energies, which would enable Zamara to persist. She used the Alys'aril's energies to trap Ulrezaj within her crystal. The battle fell to the Dominion, which defeated the zerg. A badly-wounded Stewart was finished off by Selendis.

As the crystals were taken to the safety of Shakuras, Ramsey, Dahl, and Krythkal remained behind. Valerian Mengsk's forces seized the planet for the Dominion, but he needed a way to save Ramsey; otherwise, Dominion psychics would steal what he knew and cripple his mind. Ramsey no longer had access to the knowledge but they knew Arcturus wouldn't believe that. Devon Starke proposed a solution—he mentally "attacked" Ramsey, copying some of Ramsey's memories. Pretending Ramsey's escape was his fault, he would allow himself to be turned over to Arcturus Mengsk and be killed or mentally ruined as they attempted to extract Ramsey's knowledge from him. Starke would vigorously defend what few memories he had copied in order to satisfy his interrogators.

Afterward, Ramsey's life was saved in an operation to remove the brain tumor that had developed from carrying Zamara's mind. The protoss had returned to Ehlna with a massive fleet, forcing a Dominion retreat. Ramsey was finally able to tell Valerian Mengsk about his adventures.